With its cozy bakeries and candlelit restaurants, tree-lined Bedford St. is a picture-perfect piece of the West Village. But upon second glance, there is something missing. In front of 12 Bedford St. sits an empty tree pit. Home to a male gingko for nearly 20 years, all that remains is a dirt-covered stump and a yellow, laminated sign that reads:

In the wake of Mayor Mike Bloomberg’s recently launched Million Trees NYC initiative to plant and care for 1 million trees throughout the five boroughs in the next decade, the residents of 12 Bedford are confused and angered as to how their loss fits into this picture.

On Nov. 15, Stu Waldman and Livvie Mann were on their way out to an event at the Javits Center when Waldman noticed through their front window two people pruning their beloved tree. He and his wife had paid for it to be planted when they first moved to Bedford St. Having received no call ahead of time from the Parks Department, Waldman and Mann rushed out to find out who the pruners were and what exactly they were up to. Waldman said there was no indication on their uniforms that the man and woman worked for the Parks Department. But the pair of pruners said they were hired by the city to cut down the tree because it was cracked and posed a danger to local residents.

After a few minutes of arguing, the couple — hoping they had convinced the pruners to consult with their supervisor before going through with the job — left for their evening event. When they returned later that night, the tree was gone.

As they retold the story recently, they sat perched on their side-by-side sofa chairs, finishing each other’s sentences. When they came to the moment when they found the tree gone, they gazed wistfully out at the empty space where it once stood.

“We were upset, felt violated and lied to,” Mann said. “Everything about that tree represented years of work. It’s not easy to keep up a tree around here.”

Sasha Acosta-Cohen, manager of the Blue Ribbon Bakery next door to 12 Bedford St., was still at work when the tree went down. As he recounted the story of its removal, a young couple who live across the street looked up from their mugs of hot chocolate to listen. They, too, had been wondering what happened to that tree.

“I thought the guy was just trimming it. Then slowly but surely he whittled it away, and it was just a stump,” Acosta-Cohen said. “The tree was perfectly healthy. There was just a little crack on top, but it definitely didn’t look dangerous.”

Acosta-Cohen and Waldman and Mann have called in complaints to the 311 phone line and received no response thus far. Mann, who has served as president of the Bedford Downing Block Association for the past 10 years, worked closely with the Parks Department to plant trees in Washington Square Park, and is trained as a “citizen pruner.” She is exasperated over the irony that of all trees in the neighborhood, the one in front of her home would be cut down.

“I have done everything that has to do with trees in this city,” she said. “We can’t bring the tree back at this point, but I’d like a resolution and a better system for the entire city.”

For example, Mann suggested that residents be given at least a week’s notice so they can respond before a tree is cut down.

According to William Steyer, director of the Parks Department’s Manhattan Forestry Department, the agency does have a policy of telling residents ahead of time when a tree in front of their property is going to be cut down, unless the tree is in “emergency condition.”

“The tree was cracked all the way through, and it was only a matter of time before it would fall and injure someone,” Steyer said of the tree outside 12 Bedford. “In this case, we didn’t have time to call ahead because we had to take immediate action.”

Parks spokesperson Cristina DeLuca said a routine inspection was conducted on Nov. 14, when a Parks employee identified a split developing in the tree that could cause it to break off and hurt someone. The tree was removed the next day by two climbers and pruners employed by Parks.

“Climbers and pruners wear different uniforms than regular Parks workers, so that’s probably why they were confused,” DeLuca said.

Waldman and Mann conceded that the tree was cracked at the top and had been hit by a few delivery trucks in its time, but they maintain that it had remained sturdy and showed no signs of falling over or dying any time soon.

“Parks Department cut down a healthy tree and instead of owning up to their mistake, they’re covering themselves by lying,” Waldman said. “Of course, we can’t prove it, because they cut the evidence down.”

The pair plan to take the issue to Community Board 2 or the City Council if they don’t get a response from 311 soon. Bob Gormley, C.B. 2 district manager, said the board is working on a number of initiatives to plant trees in empty tree pits in the neighborhood, but he was surprised to hear about this particular case.

“Parks is not looking to remove trees, but to plant more of them right now,” Gormley said. “It wouldn’t make sense to put the time and money into cutting down a tree unless there was a real problem.”

When a tree is removed by the Parks Department, it automatically becomes a planting site for the next planting season, which will occur this spring.

“We realize how many people care about this tree and will try to replant it immediately,” Steyer said.

And when it grows, the new tree on Bedford St. will be one in a million.